PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3H54
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (147 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE,COMPLEX WITH GALNAC
Authors
:
N. E. Clark, S. C. Garman
Date
:
21 Apr 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycoprotein, Carbohydrate-Binding Protein, Glycosidase, Lysosomal Enzyme, (Beta/Alpha)8 Barrel, Protein-Ligand Complex, Disease Mutation, Disulfide Bond, Hydrolase, Lysosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. E. Clark, S. C. Garman
The 1. 9 A Structure Of Human Alpha-N-Acetylgalactosaminidase: The Molecular Basis Of Schindler And Kanzaki Diseases
J. Mol. Biol. V. 393 435 2009
[
close entry info
]
Hetero Components
(6, 36)
Info
All Hetero Components
1a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
1b: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A2G
2
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2
BMA
3
Ligand/Ion
BETA-D-MANNOSE
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GOL
15
Ligand/Ion
GLYCEROL
5
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ARG A:97 , HOH A:509 , HOH A:676
BINDING SITE FOR RESIDUE GOL A 1024
02
AC2
SOFTWARE
MET A:56 , GLU A:57 , ASP A:60 , TYR A:108 , HOH A:723
BINDING SITE FOR RESIDUE GOL A 1039
03
AC3
SOFTWARE
PHE A:125 , GLY A:129 , PHE A:159
BINDING SITE FOR RESIDUE GOL A 1108
04
AC4
SOFTWARE
GLY A:129
BINDING SITE FOR RESIDUE GOL A 1113
05
AC5
SOFTWARE
THR A:25 , PRO A:26 , PRO A:27 , MET A:28 , GLY A:71 , THR A:73 , TYR A:74 , HOH A:804
BINDING SITE FOR RESIDUE GOL A 1165
06
AC6
SOFTWARE
TYR A:192 , ASP A:216 , ASP A:217 , HOH A:708 , A2G A:1000
BINDING SITE FOR RESIDUE GOL A 1200
07
AC7
SOFTWARE
TRP A:33 , CYS A:127 , MET A:128 , ASP A:217 , HOH A:709 , A2G A:1000
BINDING SITE FOR RESIDUE GOL A 1201
08
AC8
SOFTWARE
ARG A:344 , THR A:345 , ASP A:346 , GLN B:219
BINDING SITE FOR RESIDUE GOL A 1328
09
AC9
SOFTWARE
ASN A:48 , ASP A:285 , ARG A:287 , THR A:288
BINDING SITE FOR RESIDUE GOL A 1030
10
BC1
SOFTWARE
LEU A:226 , ASN A:230 , VAL A:233 , GLU A:325 , TYR A:327
BINDING SITE FOR RESIDUE GOL A 1210
11
BC2
SOFTWARE
ASN A:124 , PHE A:159 , NAG A:625 , FUC A:627 , HOH A:657 , HOH A:660 , HOH A:707
BINDING SITE FOR RESIDUE NAG A 624
12
BC3
SOFTWARE
HOH A:578 , NAG A:624 , BMA A:626 , HOH A:657
BINDING SITE FOR RESIDUE NAG A 625
13
BC4
SOFTWARE
PHE A:159 , HOH A:578 , NAG A:625
BINDING SITE FOR RESIDUE BMA A 626
14
BC5
SOFTWARE
NAG A:624
BINDING SITE FOR RESIDUE FUC A 627
15
BC6
SOFTWARE
ASP A:19 , ASN A:177 , GLY A:180 , ARG A:181 , HOH A:481 , HOH A:587 , NAG A:678 , HOH A:760 , HOH A:761 , HOH A:803
BINDING SITE FOR RESIDUE NAG A 677
16
BC7
SOFTWARE
ASP A:19 , GLY A:21 , HOH A:426 , NAG A:677 , BMA A:679 , MAN A:681 , HOH A:790
BINDING SITE FOR RESIDUE NAG A 678
17
BC8
SOFTWARE
HOH A:569 , NAG A:678 , MAN A:680 , MAN A:681 , HOH A:701 , ARG B:61 , GLN B:64 , ASP B:65
BINDING SITE FOR RESIDUE BMA A 679
18
BC9
SOFTWARE
BMA A:679 , HOH A:719 , HOH A:730
BINDING SITE FOR RESIDUE MAN A 680
19
CC1
SOFTWARE
NAG A:678 , BMA A:679
BINDING SITE FOR RESIDUE MAN A 681
20
CC2
SOFTWARE
GLU A:383 , ASN A:385 , HOH A:451 , HOH A:516 , HOH A:609 , HOH A:724
BINDING SITE FOR RESIDUE NAG A 885
21
CC3
SOFTWARE
HOH A:12 , TRP A:33 , ASP A:78 , ASP A:79 , TYR A:119 , CYS A:127 , MET A:128 , LYS A:154 , ASP A:156 , SER A:188 , ALA A:191 , ARG A:213 , ASP A:217 , HOH A:708 , GOL A:1200 , GOL A:1201
BINDING SITE FOR RESIDUE A2G A 1000
22
CC4
SOFTWARE
ILE B:40 , ASN B:41 , ASP B:43
BINDING SITE FOR RESIDUE GOL B 1024
23
CC5
SOFTWARE
GLY B:129
BINDING SITE FOR RESIDUE GOL B 1108
24
CC6
SOFTWARE
MET B:128 , TYR B:130
BINDING SITE FOR RESIDUE GOL B 1113
25
CC7
SOFTWARE
ALA B:191 , TYR B:192 , ASP B:216 , ASP B:217 , A2G B:2000
BINDING SITE FOR RESIDUE GOL B 1200
26
CC8
SOFTWARE
ARG A:37 , GLN A:219 , ARG B:344 , THR B:345 , ASP B:346
BINDING SITE FOR RESIDUE GOL B 1328
27
CC9
SOFTWARE
ASN B:124 , HOH B:525 , NAG B:625 , FUC B:627 , HOH B:629
BINDING SITE FOR RESIDUE NAG B 624
28
DC1
SOFTWARE
HOH B:565 , NAG B:624 , FUC B:627
BINDING SITE FOR RESIDUE NAG B 625
29
DC2
SOFTWARE
HOH B:531 , NAG B:624 , NAG B:625
BINDING SITE FOR RESIDUE FUC B 627
30
DC3
SOFTWARE
ARG A:199 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , ARG B:181 , HOH B:463 , HOH B:478 , HOH B:530 , HOH B:538 , HOH B:648 , NAG B:678
BINDING SITE FOR RESIDUE NAG B 677
31
DC4
SOFTWARE
ASP B:19 , GLY B:21 , NAG B:677 , BMA B:679 , MAN B:681
BINDING SITE FOR RESIDUE NAG B 678
32
DC5
SOFTWARE
NAG B:678 , MAN B:680 , MAN B:681
BINDING SITE FOR RESIDUE BMA B 679
33
DC6
SOFTWARE
BMA B:679 , HOH B:697
BINDING SITE FOR RESIDUE MAN B 680
34
DC7
SOFTWARE
NAG B:678 , BMA B:679 , HOH B:728
BINDING SITE FOR RESIDUE MAN B 681
35
DC8
SOFTWARE
GLU B:383 , ASN B:385
BINDING SITE FOR RESIDUE NAG B 885
36
DC9
SOFTWARE
TRP B:33 , ASP B:78 , ASP B:79 , TYR B:119 , CYS B:127 , MET B:128 , LYS B:154 , ASP B:156 , SER B:188 , ARG B:213 , ASP B:217 , HOH B:435 , HOH B:457 , GOL B:1200
BINDING SITE FOR RESIDUE A2G B 2000
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_000496 (S160C, chain A/B, )
2: VAR_000497 (E325K, chain A/B, )
3: VAR_022525 (R329Q, chain A/B, )
4: VAR_000498 (R329W, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_000496
S
160
C
NAGAB_HUMAN
Disease (SCHIND)
121434532
A/B
S
160
C
2
UniProt
VAR_000497
E
325
K
NAGAB_HUMAN
Disease (SCHIND)
---
A/B
E
325
K
3
UniProt
VAR_022525
R
329
Q
NAGAB_HUMAN
Disease (KANZD)
121434533
A/B
R
329
Q
4
UniProt
VAR_000498
R
329
W
NAGAB_HUMAN
Disease (KANZD)
---
A/B
R
329
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ALPHA_GALACTOSIDASE (A:71-86,B:71-86)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
NAGAB_HUMAN
71-86
2
A:71-86
B:71-86
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3h54a2 (A:310-404)
1b: SCOP_d3h54b2 (B:310-404)
2a: SCOP_d3h54a1 (A:18-309)
2b: SCOP_d3h54b1 (B:18-309)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d3h54a2
A:310-404
1b
d3h54b2
B:310-404
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Amylase, catalytic domain
(385)
Protein domain
:
automated matches
(71)
Human (Homo sapiens) [TaxId: 9606]
(13)
2a
d3h54a1
A:18-309
2b
d3h54b1
B:18-309
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3h54A01 (A:18-307)
1b: CATH_3h54B01 (B:18-307)
2a: CATH_3h54A02 (A:314-404)
2b: CATH_3h54B02 (B:314-404)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Human (Homo sapiens)
(78)
1a
3h54A01
A:18-307
1b
3h54B01
B:18-307
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Human (Homo sapiens)
(76)
2a
3h54A02
A:314-404
2b
3h54B02
B:314-404
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (156 KB)
Header - Asym.Unit
Biol.Unit 1 (147 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3H54
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help